Skip to content

Commit

Permalink
implement basic checks; use ECMAScript for regex
Browse files Browse the repository at this point in the history
  • Loading branch information
@mr-c
mr-c committed May 11, 2022
1 parent a3b0e77 commit c6c9fe5
Show file tree
Hide file tree
Showing 4 changed files with 162 additions and 7 deletions.
11 changes: 8 additions & 3 deletions cwltool/extensions-v1.2.yml
View file
Original file line number Diff line number Diff line change
Expand Up @@ -199,8 +199,7 @@ $graph:
- name: regex
type: record
doc: |
Regular Expression
TODO: what type of regex?
ECMAScript 5.1 Regular Expression constraint.
fields:
class:
type:
Expand All @@ -213,7 +212,13 @@ $graph:
_type: "@vocab"
rpattern:
type: string

doc: |
Testing should be the equivalent of calling `/rpattern/.test(value)`
where `rpattern` is the value of the `rpattern` field, and `value`
is the input object value to be tested. If the result is `true` then the
input object value is accepted. If the result if `false` then the
input object value does not match this constraint.
<https://262.ecma-international.org/5.1/#sec-15.10.6.3>
- name: Restrictions
type: record
Expand Down
105 changes: 101 additions & 4 deletions cwltool/process.py
View file
Original file line number Diff line number Diff line change
Expand Up @@ -20,6 +20,7 @@
Iterable,
Iterator,
List,
Mapping,
MutableMapping,
MutableSequence,
Optional,
Expand Down Expand Up @@ -55,6 +56,7 @@
from .loghandler import _logger
from .mpi import MPIRequirementName
from .pathmapper import MapperEnt, PathMapper
from .sandboxjs import execjs
from .secrets import SecretStore
from .stdfsaccess import StdFsAccess
from .update import INTERNAL_VERSION, ORIGINAL_CWLVERSION
Expand Down Expand Up @@ -523,10 +525,11 @@ def var_spool_cwl_detector(
r = False
if isinstance(obj, str):
if "var/spool/cwl" in obj and obj_key != "dockerOutputDirectory":
debug = _logger.isEnabledFor(logging.DEBUG)
_logger.warning(
SourceLine(item=item, key=obj_key, raise_type=str).makeError(
_VAR_SPOOL_ERROR.format(obj)
)
SourceLine(
item=item, key=obj_key, raise_type=str, include_traceback=debug
).makeError(_VAR_SPOOL_ERROR.format(obj))
)
r = True
elif isinstance(obj, MutableMapping):
Expand Down Expand Up @@ -743,7 +746,9 @@ def __init__(
and not is_req
):
_logger.warning(
SourceLine(item=dockerReq, raise_type=str).makeError(
SourceLine(
item=dockerReq, raise_type=str, include_traceback=debug
).makeError(
"When 'dockerOutputDirectory' is declared, DockerRequirement "
"should go in the 'requirements' section, not 'hints'."
""
Expand Down Expand Up @@ -805,6 +810,98 @@ def _init_job(
vocab=INPUT_OBJ_VOCAB,
)

restriction_req, mandatory_restrictions = self.get_requirement(
"ParameterRestrictions"
)

if restriction_req:
restrictions = restriction_req["restrictions"]
for entry in cast(List[CWLObjectType], restrictions):
name = shortname(cast(str, entry["input"]))
if name in job:
value = job[name]
matched = False
for constraint in cast(
List[CWLOutputType], entry["constraints"]
):
if isinstance(constraint, Mapping):
if constraint["class"] == "intInterval":
if not isinstance(value, int):
raise SourceLine(
constraint,
None,
WorkflowException,
runtime_context.debug,
).makeError(
"intInterval parameter restriction is only valid for inputs of type 'int'; "
f"instead got {type(value)}: {value}."
)
low = cast(
Union[int, float],
constraint.get("low", -math.inf),
)
high = cast(
Union[int, float],
constraint.get("high", math.inf),
)
matched = value >= low and value <= high
elif constraint["class"] == "realInterval":
if not isinstance(value, (int, float)):
raise SourceLine(
constraint,
None,
WorkflowException,
runtime_context.debug,
).makeError(
"realInterval parameter restriction is only valid for inputs of type 'int', 'float', and 'double'; "
f"instead got {type(value)}: {value}."
)
low = cast(
Union[int, float],
constraint.get("low", -math.inf),
)
high = cast(
Union[int, float],
constraint.get("high", math.inf),
)
low_inclusive = constraint.get(
"low_inclusive", True
)
high_inclusive = constraint.get(
"high_inclusive", True
)
check_low = (
value >= low if low_inclusive else value > low
)
check_high = (
value <= high if low_inclusive else value < high
)
matched = check_low and check_high
elif constraint["class"] == "regex":
rpattern = constraint["rpattern"]
quoted_value = json.dumps(value)
matched = cast(
bool,
execjs(
f"/{rpattern}/.test({quoted_value})",
"",
runtime_context.eval_timeout,
runtime_context.force_docker_pull,
),
)
elif constraint == value:
matched = True
if matched:
break
if not matched:
raise SourceLine(
job, name, WorkflowException, runtime_context.debug
).makeError(
f"The field '{name}' is not valid because its "
f"value '{value}' failed to match any of the "
f"constraints '{json.dumps(entry['constraints'])}'."
)

if load_listing and load_listing != "no_listing":
get_listing(fs_access, job, recursive=(load_listing == "deep_listing"))

Expand Down
5 changes: 5 additions & 0 deletions tests/parameter_restrictions.cwl
View file
Original file line number Diff line number Diff line change
Expand Up @@ -7,6 +7,7 @@ doc: |
inputs:
one: double
two: string
three: int


hints:
Expand All @@ -24,6 +25,10 @@ hints:
two:
- class: cwltool:regex
rpattern: "foo.*bar"
three:
- class: cwltool:intInterval
low: -10
high: -7


baseCommand: echo
Expand Down
48 changes: 48 additions & 0 deletions tests/test_ext.py
View file
Original file line number Diff line number Diff line change
Expand Up @@ -295,3 +295,51 @@ def test_warn_large_inputs() -> None:
)
finally:
cwltool.process.FILE_COUNT_WARNING = was


def test_parameter_restrictions_parsing() -> None:
"""Basic parsing of the ParameterRestrictions extension."""
assert (
main(
["--enable-ext", "--validate", get_data("tests/parameter_restrictions.cwl")]
)
== 0
)


def test_parameter_restrictions_valid_job() -> None:
"""Confirm that valid values are accepted."""
assert (
main(
[
"--enable-ext",
get_data("tests/parameter_restrictions.cwl"),
"--one",
"2.5",
"--two",
"foofoobar",
"--three",
"-5",
]
)
== 0
)


def test_parameter_restrictions_invalid_job() -> None:
"""Confirm that an invvalid value is rejected."""
assert (
main(
[
"--enable-ext",
get_data("tests/parameter_restrictions.cwl"),
"--one",
"2.5",
"--two",
"fuzzbar",
"--three",
"-5",
]
)
== 1
)

0 comments on commit c6c9fe5

Please sign in to comment.